Shallow brackish water is widely distributed throughout north and northwest China and could be rational used. To evaluate the spatial distribution and variability of cotton field salinity under mulched drip irrigation with brackish and fresh water in southern Xinjiang, electromagnetic induction EM38-MK2 was applied to measure the apparent soil electrical conductivity. Statistical characteristics of soil salinity from the interpretation models of soil salinity showed that the scenario of brackish water irrigation had the higher salinity level and the lower variation coefficient than the fresh water irrigation. The optimal semi-variance models of brackish water and fresh water irrigation were exponential and Gaussian models respectively. Both models were characterized by strong spatial correlation. Compared with fresh water irrigation, the scenario of brackish water irrigation with the higher salinity level had the lager range variation and increased the spatial dependency of soil salinity. The spatial distribution of field salinity interpolated by Kriging method showed that both scenarios of brackish and fresh water irrigation had some filed parts with high salinity level, which would affect cotton emergence. EM38-MK2 would be suggested to investigate the field salinity distribution. According to soil salinity levels of different parts, amount of fresh water of flood irrigation for leaching salinity could be defined to save water and ensure the agriculture production.